custom designed oligo dnas  (Integrated DNA Technologies)

Journal: Nature Communications

Article Title: Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons

doi: 10.1038/s41467-022-31336-x

Figure Lengend Snippet: a Schematic illustration of the CycMIST process to analyze multiple proteins through the MIST microbeads array. b Distribution of the number of oligo DNA-coated microbeads on each 75 μm × 75 μm area of a MIST array that is corresponding to a PDMS microwell, n = 3 independent MIST array. c Distribution of the number of same kind oligo DNA-coated microbeads on the same MIST array, n = 5 independent MIST array. d Characterization of the CycMIST sensitivity by varying the concentrations of 50 biotinylated complementary oligo DNAs on the MIST array, n = 10 independent experiments. This is the same procedure in single-cell protein detection experiments except cell loading and conjugate binding. e Consistency of fluorescence intensities for 4 decoding cycles and for 3 fluorescent color dyes (Alexa Fluor 488, Cy3 and Cy5), n = 5 independent experiments. f Sample images of multiplexed assay of 50 proteins from a single cell by CycMIST and the 4 decoding cycles images. The greyscale images are protein detection result, and the color images are the decoding cycles from cycle 1 to cycle 4. The bottom panel is the zoom-in images from the squares in the up panel. Scale bar: 20 μm (up panel); 5 μm (bottom panel). Data are presented as mean values ± SD of more than three independent experiments, and error bars are within symbol size if not shown. The term (arb. units) is abbreviated for arbitrary units.

Article Snippet: Custom designed oligo DNAs were purchased from Integrated DNA Technologies and used as received.

Techniques: Binding Assay, Fluorescence

Journal: BMC Genomics

Article Title: Global transcriptional response of Caulobacter crescentus to iron availability

doi: 10.1186/1471-2164-14-549

Figure Lengend Snippet: Overview of iron-responsive and Fur-regulated genes in C. crescentus identified by microarray analyses. The Venn diagrams were constructed using the number of up- and down-regulated genes from experiments comparing wild type cells exposed to iron-limiting versus iron-replete conditions or comparing fur mutant strain versus wild type strain both in iron-replete condition. The complete set of the genes belonging to each group is listed in Tables , , , and Additional file : Table S1. The upstream region of these genes (−200 to +50 bp relative to the start codon) were searched for sequence motifs using the MEME tool. A 19-pb palindromic motif, corresponding to the Fur binding site, was exclusively found in the group of genes regulated by both iron and Fur.

Article Snippet: Labeled cDNA samples were hybridized to a custom-designed DNA oligo microarray (Agilent) (each gene is covered by 9–11 probes located −300 to +200 relative to the translational start site) using a protocol previously described [ , ].

Techniques: Microarray, Construct, Mutagenesis, Sequencing, Binding Assay

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: The 20 most strongly regulated non-MHC/non-NKC genes in allogeneic skin explants compared to syngeneic controls as revealed by the microarray experiment.

Article Snippet: For the expression profiling, a custom-designed oligo DNA microarray (Agilent) was used.

Techniques: Microarray, Sequencing, Derivative Assay

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: A subgroup of 8 samples used for the microarray experiment (see Fig. 1 ) was analyzed by qRT-PCR for the expression of 10 MHC and 3 NKC genes. The ΔΔct value was calculated, i.e. the Δct ( Gapdh – gene of interest) of the allogeneic skin explant samples minus Δct ( Gapdh – gene of interest) of the corresponding control sample. The control sample was either a parallel skin explant exposed to syngeneic lymphocytes as in the microarray experiment (syngeneic control, black bars) or a parallel skin explant sample cultured in medium only (medium control, white bars). The means of the ΔΔct values plus standard errors of the mean (SEM) are shown. A positive value indicates an up-regulation of gene expression in the allogeneic samples.

Article Snippet: For the expression profiling, a custom-designed oligo DNA microarray (Agilent) was used.

Techniques: Microarray, Quantitative RT-PCR, Expressing, Cell Culture

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Agreement between qPCR and microarray data

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Least-squares regression fit between microarray and qPCR data. The fit between microarray and qPCR non-normalised (non) and normalised (TEF) Log2FC (Fold Change) is shown in respect to the identity line (dashed) for the selected target genes of T. thynnus

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Combined expression profiles of target genes belonging to six largest T. thynnus tissue clusters. The profiles were derived by combining qPCR and microarray data for specific genes using their respective percentile ranks. Nonparametric Kruskal-Wallis test was used to determine statistical significance of the differences between tissues. Letter codes denote statistical significance at p < 0.05

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Expressing, Derivative Assay, Microarray